Bulk RNA-seq ITK-SYK
Filtered data, DEG
RNA-seq
Filtering
Count matrix : This count matrix was modified like followings.
B cell genes out (Cd79a, Cd79b, Jchain)
Immunoglobulin genes out
“Ighv* ,”Igl* , “Igk*
Genes like”Igf* , “Igl* (Starting with Ig- but not Immunoglobulin
genes) are not removed (checked manually)
TPM table (all genes)
PCA
PCA plot
PCA plot by condition
PCA plot version 3
Updated part from here
DEG analysis
DEG 1B vs S
- DEG information table
- Volcanoplot
- Detailed information table
DEG 2B vs S
DEG information table
Volcanoplot
Detailed information table
Overlapping genes
From following two comparisons, significants genes(showing either up-regulation or down-regulation) were obtained.
- DEG_1B_S
- DEG_2B_S
Venn Diagram
Upset plot
Gene information table
Information of table
- DEG_1BvsS : DEGs from 1B/S
- DEG_2BvsS : DEGs from 2B/S
- Shared : overlapping genes between 1B/S and 2B/S
GSEA
GSEA with overlapping genes’ differential expression between
samples.
Overlapping genes include both up-regulated genes and down-regulated
genes.
DEG 1B/S
List
1. GSEA plot colored by adjusted p value
2. GSEA plot colored by significance (FDR <= 0.05)
3. GSEA detail table
DEG 2B/S
List
1. GSEA plot colored by adjusted p value
2. GSEA plot colored by significance (FDR <= 0.05)
3. GSEA detail table.
Selected pathway analysis in 2B/S
IL6_JAK_STAT3_SIGNALING
INFLAMMATORY RESPONSE
This part is added 24.05.01
Overlapping genes (up-regulated only)
Venn Diagram
Up regualted genes
Upset plot
Up regualted genes
Gene information table
Up regualted genes
Information of table
- DEG_1BvsS : DEGs from 1B/S
- DEG_2BvsS : DEGs from 2B/S
- Shared : overlapping genes between 1B/S and 2B/S
DEG UP 1B/S
List
1. GSEA plot colored by adjusted p value
2. GSEA plot colored by significance (FDR <= 0.05)
3. GSEA detail table
DEG UP 2B/S
List
1. GSEA plot colored by adjusted p value
2. GSEA plot colored by significance (FDR <= 0.05)
3. GSEA detail table.
Overlapping genes (down-regulated only)
Venn Diagram
DN regualted genes
Upset plot
DN regualted genes
Gene information table
DN regualted genes
Information of table
- DEG_1BvsS : DEGs from 1B/S
- DEG_2BvsS : DEGs from 2B/S
- Shared : overlapping genes between 1B/S and 2B/S
DEG Down 1B/S
List
1. GSEA plot colored by adjusted p value
2. GSEA plot colored by significance (FDR <= 0.05)
3. GSEA detail table
DEG Down 2B/S
List
1. GSEA plot colored by adjusted p value
2. GSEA plot colored by significance (FDR <= 0.05)
3. GSEA detail table.